I would stay away from the USB storage for this, but grab a SATA disk that you may have (or buy one). Put that into the hosts and format it as a VMFS5 datastore. If you have vCenter, you can do a Storage vMotion / Migration of the guests. Otherwise you can copy the VM folder from one datastore to another. If required, you can put the disk in any host, move the files back, or even just boot the guest up from that disk.
Your other option (with USB) would be to export the VM or download the files via your local computer (to which the USB drive is connected and available) to the USB drive.
Regarding your other questions:
1) Yes, copy the entire folder to make sure that you have every required file. You can skip a few if you need to, but if you have the space, just take it all.
2) Once you have copied the files back to the original datastore, you can use the datastore browser to browse to the folder of the VM you want to start. In this folder, you will find a file with the VM name and the extension .vmx. You can right click this file and say add to inventory. It will then be added back to vCenter / your ESXi host.
